TOPIC MODELING WITH NATURAL LANGUAGE PROCESSING FOR IDENTIFICATION OF NUCLEAR PROLIFERATION-RELEVANT SCIENTIFIC AND TECHNICAL PUBLICATIONS.
Abstract not provided.
Bisila, Jonathan↗
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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Leveraging Natural Language Processing and Generative Models in Molecular Chemistry: Property Prediction and Novel Compound Generation
The accurate prediction of molecular properties is important for the rational design and the advancement of green chemistry and sustainable materials research. However, the predictive power of traditional computational chemistry methods is limited due to computational restrictions. Here, in this study, we examine an alternative approach to the accurate prediction of properties of organic compounds: natural language processing (NLP)-based molecular embedding. Using viscosity, partition coefficient (log P), and enthalpy of vaporization as test properties through a survey of comprehensive datasets comprising 5695 data points for viscosity, 25 870 data points for log P, and 2296 data points for enthalpy of vaporization. These are important properties for the design of greener, safer, and sustainable chemical processes. Models were trained using NLP methods such as Mol2vec and fine-tuned ChemBERTa, and results were compared with traditional input featurization techniques such as Morgan fingerprints and quantum chemistry derived sigma profiles and DFT features. Among the various machine learning models, Mol2vec demonstrated superior predictive capabilities, achieving the highest correlation coefficient (R 2 = 0.945) and lowest RMSE (0.106 mPa s) for viscosity, as well as high accuracy for log P and enthalpy of vaporization predictions. These findings establish the Mol2vec featurization technique, graph-convolutional neural networks (GCNN), and fine-tuned ChemBERTa model as powerful tools for predictive modeling of organic compounds properties, offering a significant improvement over previously used featurization techniques and opening up strategies for very-high-throughput computational screening. Finally, we integrated ML models with hybrid language-model-based generative adversarial networks (LM-GAN) to generate novel molecular sequences with desirable properties for different research applications. The ability to computationally design solvents with lower viscosity, lower log P, and lower enthalpy of vaporization offers a data-driven route to accelerating the discovery of sustainable alternatives to traditionally toxic solvents.
ChemBERTa↗
An agentic artificially intelligent X-ray scientist
Executing experimental tasks in both normal research laboratories and large-scale scientific facilities often requires extensive human supervision and remains a key challenge on the path to fully autonomous, artificial intelligence (AI)-driven science. Here we demonstrate a large language model-driven agent that autonomously performs X-ray sample alignment on a synchrotron beamline by planning actions, executing instrumental commands, interpreting observations and iterating towards experimental goals. Based on existing large language models with structured tool-use via the model context protocol, our AI X-ray scientist was guided and tested using an in-house-built virtual experimental setup that mirrors a six-circle diffractometer at an operational synchrotron beamline. The agentic workflow developed in the virtual environment was directly deployed on a real beamline, where it correctly identified reference reflections and determined the orientation matrix, an essential first step in any type of single-crystal scattering experiment. Our AI X-ray scientist responded effectively to unexpected experimental conditions, demonstrating adaptive problem-solving and readiness for addressing practical experimental situations. Our study provides a step towards autonomous operation across diverse experimental environments at large-scale scattering facilities.
Chen, Zhantao (ORCID:0000000319543868)↗
NEPATEC2.0: NEPA Text Corpus v2.0
The National Environmental Policy Act of 1969, as amended (NEPA), is a major environmental law in the United States, requiring Federal agencies to consider and document potential environmental impacts before deciding on a proposed action. Modernization of NEPA and permitting processes faces significant challenges due to the lack of standardized formats and interoperable systems for organizing and sharing NEPA-related information across agencies. Much of the information gathered during NEPA reviews is written into documents such as categorical exclusions, environmental assessments, and environmental impact statements, then filed in predominately independent agency file stores that may or may not be publicly accessible. The application of metadata and data standards, such as those recommended by the Council on Environmental Quality (CEQ), to NEPA documents offers a shared vocabulary and structure for key entities like projects, processes, and documents that can streamline information exchange and enhance collaboration across systems. In this work, we publicly release NEPATEC2.0, an expanded corpus of NEPA documents with associated metadata. NEPATEC2.0 encompasses approximately 120,000 documents from 60,000 projects prepared by more than 60 different agencies. Modeled to align with CEQ metadata standards, NEPATEC2.0 promotes consistency in environmental reviews and supports the ongoing effort to modernize permitting technologies by facilitating more transparent, efficient, and data-driven decision-making. Importantly, NEPATEC2.0 demonstrates the possibilities and limitations of large language model-based prompting to extract information from NEPA documents at scale.
environmental review↗
Certain aspects of the psychological analysis of programmer activity
The psychological analysis of programmer activity showed that one of its basic characteristics is the need to employ formal languages. In determining ways of effectively mastering the capacity to write algorithms in the algorithmic language, it is expedient to proceed from its similarity to the living languages and the language of mathematical formulas, and to choose certain psychological principles of mastering foreign languages and mathematical symbols in teaching the algorithmic language. General models of the input language significantly increase the effectiveness of its mastery and permit the development of thinking on the part of the students.
Bondarovskaya, V. M.↗
A development framework for distributed artificial intelligence
The authors describe distributed artificial intelligence (DAI) applications in which multiple organizations of agents solve multiple domain problems. They then describe work in progress on a DAI system development environment, called SOCIAL, which consists of three primary language-based components. The Knowledge Object Language defines models of knowledge representation and reasoning. The metaCourier language supplies the underlying functionality for interprocess communication and control access across heterogeneous computing environments. The metaAgents language defines models for agent organization coordination, control, and resource management. Application agents and agent organizations will be constructed by combining metaAgents and metaCourier building blocks with task-specific functionality such as diagnostic or planning reasoning. This architecture hides implementation details of communications, control, and integration in distributed processing environments, enabling application developers to concentrate on the design and functionality of the intelligent agents and agent networks themselves.
Adler, Richard M.↗
Model-Based Verification and Validation of Spacecraft Avionics
Our simulation was able to mimic the results of 30 tests on the actual hardware. This shows that simulations have the potential to enable early design validation - well before actual hardware exists. Although simulations focused around data processing procedures at subsystem and device level, they can also be applied to system level analysis to simulate mission scenarios and consumable tracking (e.g. power, propellant, etc.). Simulation engine plug-in developments are continually improving the product, but handling time for time-sensitive operations (like those of the remote engineering unit and bus controller) can be cumbersome.
Systems Modeling Language (SysML↗
Advanced communication system time domain modeling techniques ASYSTD software description. Volume 2: Program support documentation
The theoretical basis for the ASYSTD program is discussed in detail. In addition, the extensive bibliography given in this document illustrates some of the extensive work accomplished in the area of time domain simulation. Additions have been in the areas of modeling and language program enhancements, orthogonal transform modeling, error analysis, general filter models, BER measurements, etc. Several models have been developed which utilize the COMSAT generated orthogonal transform algorithms.
Source record↗
Using a simulation assistant in modeling manufacturing systems
Numerous simulation languages exist for modeling discrete event processes, and are now ported to microcomputers. Graphic and animation capabilities were added to many of these languages to assist the users build models and evaluate the simulation results. With all these languages and added features, the user is still plagued with learning the simulation language. Futhermore, the time to construct and then to validate the simulation model is always greater than originally anticipated. One approach to minimize the time requirement is to use pre-defined macros that describe various common processes or operations in a system. The development of a simulation assistant for modeling discrete event manufacturing processes is presented. A simulation assistant is defined as an interactive intelligent software tool that assists the modeler in writing a simulation program by translating the modeler's symbolic description of the problem and then automatically generating the corresponding simulation code. The simulation assistant is discussed with emphasis on an overview of the simulation assistant, the elements of the assistant, and the five manufacturing simulation generators. A typical manufacturing system will be modeled using the simulation assistant and the advantages and disadvantages discussed.
Schroer, Bernard J.↗
PRIME: Protein Representation Inference for Mutation Evaluation
Protein language machine learning models built upon existing ESM-2 model developed by Evolutionary Scale (evolutionaryscale.ai) and an in-house protein language model based on the BERT model developed by Google. The code also includes model training scripts and saved checkpoints from our own training using publicly available SARS-CoV-2 protein sequences.
Gibson, Kaetlyn [Los Alamos National Lab]↗
Investigating System Dependability Modeling Using AADL
This report describes Architecture Analysis & Design Language (AADL) models for a diverse set of fault-tolerant, embedded data networks and describes the methods and tools used to created these models. It also includes error models per the AADL Error Annex. Some networks were modeled using Error Detection Isolation Containment Types (EDICT). This report gives a brief description for each of the networks, a description of its modeling, the model itself, and evaluations of the tools used for creating the models. The methodology includes a naming convention that supports a systematic way to enumerate all of the potential failure modes.
Hall, Brendan↗
Reactive system verification case study: Fault-tolerant transputer communication
A reactive program is one which engages in an ongoing interaction with its environment. A system which is controlled by an embedded reactive program is called a reactive system. Examples of reactive systems are aircraft flight management systems, bank automatic teller machine (ATM) networks, airline reservation systems, and computer operating systems. Reactive systems are often naturally modeled (for logical design purposes) as a composition of autonomous processes which progress concurrently and which communicate to share information and/or to coordinate activities. Formal (i.e., mathematical) frameworks for system verification are tools used to increase the users' confidence that a system design satisfies its specification. A framework for reactive system verification includes formal languages for system modeling and for behavior specification and decision procedures and/or proof-systems for verifying that the system model satisfies the system specifications. Using the Ostroff framework for reactive system verification, an approach to achieving fault-tolerant communication between transputers was shown to be effective. The key components of the design, the decoupler processes, may be viewed as discrete-event-controllers introduced to constrain system behavior such that system specifications are satisfied. The Ostroff framework was also effective. The expressiveness of the modeling language permitted construction of a faithful model of the transputer network. The relevant specifications were readily expressed in the specification language. The set of decision procedures provided was adequate to verify the specifications of interest. The need for improved support for system behavior visualization is emphasized.
Crane, D. Francis↗
NEPATEC v2.0: Standardized Metadata and Text Corpus of National Environmental Policy Act Documents
The National Environmental Policy Act of 1969, as amended (NEPA), is a major environmental law in the United States, requiring Federal agencies to consider and document potential environmental impacts before deciding on a proposed action. Modernization of NEPA and permitting processes faces significant challenges due to the lack of standardized formats and interoperable systems for organizing and sharing NEPA-related information across agencies. Much of the information gathered during NEPA reviews is written into documents such as categorical exclusions, environmental assessments, and environmental impact statements, then filed in predominately independent agency file stores that may or may not be publicly accessible. The application of metadata and data standards, such as those recommended by the Council on Environmental Quality (CEQ), to NEPA documents offers a shared vocabulary and structure for key entities like projects, processes, and documents that can streamline information exchange and enhance collaboration across systems. In this work, we publicly release NEPATEC2.0, an expanded corpus of NEPA documents with associated metadata. NEPATEC2.0 encompasses approximately 120,000 documents from 60,000 projects prepared by more than 60 different agencies. Modeled to align with CEQ metadata standards, NEPATEC2.0 promotes consistency in environmental reviews and supports the ongoing effort to modernize permitting technologies by facilitating more transparent, efficient, and data-driven decision-making. Importantly, NEPATEC2.0 demonstrates the possibilities and limitations of large language model-based prompting to extract information from NEPA documents at scale.
54 ENVIRONMENTAL SCIENCES↗
The role of chromatin state in intron retention: A case study in leveraging large scale deep learning models
Complex deep learning models trained on very large datasets have become key enabling tools for current research in natural language processing and computer vision. By providing pre-trained models that can be fine-tuned for specific applications, they enable researchers to create accurate models with minimal effort and computational resources. Large scale genomics deep learning models come in two flavors: the first are large language models of DNA sequences trained in a self-supervised fashion, similar to the corresponding natural language models; the second are supervised learning models that leverage large scale genomics datasets from ENCODE and other sources. We argue that these models are the equivalent of foundation models in natural language processing in their utility, as they encode within them chromatin state in its different aspects, providing useful representations that allow quick deployment of accurate models of gene regulation. We demonstrate this premise by leveraging the recently created Sei model to develop simple, interpretable models of intron retention, and demonstrate their advantage over models based on the DNA language model DNABERT-2. Our work also demonstrates the impact of chromatin state on the regulation of intron retention. Using representations learned by Sei, our model is able to discover the involvement of transcription factors and chromatin marks in regulating intron retention, providing better accuracy than a recently published custom model developed for this purpose.
Biochemistry & Molecular Biology↗
Simulating an aerospace multiprocessor
The paper describes a simulator which was used to evaluate the architecture of an aerospace multiprocessor. The simulator models interactions among the processors, memories, the central data bus, and a possible 'job stack'. Special features of the simulator are discussed, including the use of explicitly coded and individually distinguishable 'job models' instead of a statistically defined 'job mix' and a specialized Job Model Definition Language to automate the detailed coding of the models. Some results are presented which show that when the simulator was employed in conjunction with queuing theory and Markov-process analysis, more insight into system behavior was obtained than would have been with any one technique alone.
Mallach, E. G.↗
Advancing Medium–and Heavy-Duty Electric Vehicle Adoption Models With Novel Natural Language Processing Metrics
Thesis to support the requirements for graduation with the degree of Master of Science in Systems Engineering.
Ouren, Fletcher↗
Modeling with Scala
The activities and the associated formalisms for modeling and programming have many commonalities. In this paper we emphasize this point of view by modeling two examples in the programming language Scala, which have previously been modeled in the VDM specification language, and the Promela modeling language of the SPIN model checker respectively. The latter Scala model uses an internal DSL for hierarchical state machines, and a simple randomized testing framework exposing the same errors as found with SPIN. We believe, as the examples illustrate, that this use of a modern programming language for modeling is promising, especially if utilizing internal DSLs.
Joshi, Rajeev↗